Locus 3611

Sequence ID	3L_DroMel_CAF1
Location	10,641,396 – 10,641,529
Length	133
Max. P	0.999351

overview

Window 7

Location	10,641,396 – 10,641,497
Length	101
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	90.40
Mean single sequence MFE	-35.50
Consensus MFE	-28.25
Energy contribution	-27.88
Covariance contribution	-0.37
Combinations/Pair	1.21
Mean z-score	-2.23
Structure conservation index	0.80
SVM decision value	1.02
SVM RNA-class probability	0.902289
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10641396 101 - 23771897
CAAACUCACCUGCAAACUCAGGUAAAUCGACACGCGUGUGUGUGUGUGUGUGCGCGGGUGAGUGGUACCUGUGUGGAGCUGACACGGCAACAAACAAAGGU
...((((((((((..((....)).....(.((((((..(....)..)))))))))))))))))...((((...((..((((...))))..)).....)))) ( -34.80)
>DroSec_CAF1 3946 99 - 1
CAAACUCACCUGCAAACUCAGGUAAAUCGACGCGCGCGUGUGUG--UGUGUGUGCGGGUGAGUGGUGCCUGUGUGGAUCUGACACGGCAACAAACAAAGGU
...(((((((((((.((....))......((((((((....)))--))))).)))))))))))(.((((.((((.......)))))))).).......... ( -37.90)
>DroEre_CAF1 3909 99 - 1
CAAACUCACCUGCAAACUCAGGUAAAUCGACACAUGUGUUUG--UGUGUGUGUGCGGGUGAGUUGUGCUUGUGUGGAGCUGACACGGCAACAAACAAAGGU
..((((((((((((.((....))......(((((..(....)--..))))).))))))))))))....((((.((..((((...))))..)).)))).... ( -33.40)
>DroYak_CAF1 3923 99 - 1
CAAACUCACCUGCAAACUCAGGUAAAUCUACGUAAGUGUGUA--UGUGUGUGCGCGGGUGAGUGGUGCCUGUGUGGAGCUGACACGGCAACAAACAAAGGU
...((((((((((..((.((.(((....(((....)))..))--).)).))..))))))))))(.((((.((((.......)))))))).).......... ( -35.90)
>consensus
CAAACUCACCUGCAAACUCAGGUAAAUCGACACACGUGUGUG__UGUGUGUGCGCGGGUGAGUGGUGCCUGUGUGGAGCUGACACGGCAACAAACAAAGGU
...((((((((((..((....))......(((((((........)))))))..))))))))))...((((((((.......))))(....)......)))) (-28.25 = -27.88 +  -0.37)

alignment

secondary structure

dotplot

Window 8

Location	10,641,435 – 10,641,529
Length	94
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	67.82
Mean single sequence MFE	-39.14
Consensus MFE	-13.54
Energy contribution	-15.22
Covariance contribution	1.68
Combinations/Pair	1.32
Mean z-score	-4.63
Structure conservation index	0.35
SVM decision value	3.53
SVM RNA-class probability	0.999351
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10641435 94 + 23771897
CUC-----ACC--CGC----GCAC-ACACACACACACACGCGUGUCGAUUUACCUGAGUUUGCAGGUGAGUUUGCCAGUGUCU-------GUGUUUGUGUGUGUGAGU-UUAGG
...-----((.--(((----((((-(((.(((((.((((..(.((.((((((((((......)))))))))).))).)))).)-------)))).)))))))))).))-..... ( -42.90)
>DroSec_CAF1 3985 86 + 1
CUC-----ACC--CGC----ACAC-ACA--CACACACGCGCGCGUCGAUUUACCUGAGUUUGCAGGUGAGUUUGCCAGUGUGU-------GUG------AUUGUGAGU-UUGGG
...-----.((--((.----((.(-(((--..(((((((((..((.((((((((((......)))))))))).))..))))))-------)))------..)))).))-.)))) ( -39.50)
>DroEre_CAF1 3948 91 + 1
CUC-----ACC--CGC----ACAC-ACACA--CAAACACAUGUGUCGAUUUACCUGAGUUUGCAGGUGAGUUUGCGUGUUUGU-------AUG--UGUGUGCGUGAGUUUUGGG
(((-----((.--.((----((((-(((.(--(((((((....((.((((((((((......)))))))))).))))))))))-------.))--))))))))))))....... ( -44.30)
>DroYak_CAF1 3962 80 + 1
CUC-----ACC--CGC----GCAC-ACACA--UACACACUUACGUAGAUUUACCUGAGUUUGCAGGUGAGUUUGCGUGU-------------------GUUUGUGAGU-UUGGG
...-----.((--((.----((.(-(((..--.((((((....(((((((((((((......)))))))))))))))))-------------------)).)))).))-.)))) ( -34.40)
>DroAna_CAF1 3520 112 + 1
AUACAGAGACAGAGACAAAAACACAACA--CACAUACAUAAGCAUAAAUCUACCUGAGUUUGCAGGUGACUAUGUCUGUGUGUUCUGCUUGUGUGUGAGUGUGUGUGUUAGAGG
...................(((((((((--(.((((((((((((.......(((((......)))))(((...))).........)))))))))))).)))).))))))..... ( -34.60)
>consensus
CUC_____ACC__CGC____ACAC_ACACACACACACACACGCGUCGAUUUACCUGAGUUUGCAGGUGAGUUUGCCUGUGUGU_______GUG__UG_GUGUGUGAGU_UUGGG
...................................(((((((.((.((((((((((......)))))))))).)).)))))))............................... (-13.54 = -15.22 +   1.68)

alignment

secondary structure

dotplot

Window 9

Location	10,641,435 – 10,641,529
Length	94
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	67.82
Mean single sequence MFE	-32.15
Consensus MFE	-8.79
Energy contribution	-9.04
Covariance contribution	0.25
Combinations/Pair	1.25
Mean z-score	-3.88
Structure conservation index	0.27
SVM decision value	3.45
SVM RNA-class probability	0.999230
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10641435 94 - 23771897
CCUAA-ACUCACACACACAAACAC-------AGACACUGGCAAACUCACCUGCAAACUCAGGUAAAUCGACACGCGUGUGUGUGUGUGU-GUGC----GCG--GGU-----GAG
.....-((((.(.((((((.((((-------(.((((((........(((((......))))).........)).)))).))))).)))-))).----).)--)))-----... ( -32.93)
>DroSec_CAF1 3985 86 - 1
CCCAA-ACUCACAAU------CAC-------ACACACUGGCAAACUCACCUGCAAACUCAGGUAAAUCGACGCGCGCGUGUGUG--UGU-GUGU----GCG--GGU-----GAG
.....-.(((((...------(((-------((((((..........(((((......)))))......(((((....))))))--)))-))))----)..--.))-----))) ( -31.50)
>DroEre_CAF1 3948 91 - 1
CCCAAAACUCACGCACACA--CAU-------ACAAACACGCAAACUCACCUGCAAACUCAGGUAAAUCGACACAUGUGUUUG--UGUGU-GUGU----GCG--GGU-----GAG
.......((((((((((((--(((-------(((((((((.....(((((((......))))).....))....))))))))--)))))-))))----)).--.))-----))) ( -39.70)
>DroYak_CAF1 3962 80 - 1
CCCAA-ACUCACAAAC-------------------ACACGCAAACUCACCUGCAAACUCAGGUAAAUCUACGUAAGUGUGUA--UGUGU-GUGC----GCG--GGU-----GAG
.....-.(((((...(-------------------(((((((.((.((((((......)))))......((....))).)).--)))))-))).----...--.))-----))) ( -26.10)
>DroAna_CAF1 3520 112 - 1
CCUCUAACACACACACUCACACACAAGCAGAACACACAGACAUAGUCACCUGCAAACUCAGGUAGAUUUAUGCUUAUGUAUGUG--UGUUGUGUUUUUGUCUCUGUCUCUGUAU
........(((.(.((....(((.(((((.((((((((.(((((((((((((......))))).))).......))))).))))--)))).))))).)))....)).).))).. ( -30.51)
>consensus
CCCAA_ACUCACACAC_CA__CAC_______ACACACAGGCAAACUCACCUGCAAACUCAGGUAAAUCGACGCACGUGUGUGUGUGUGU_GUGU____GCG__GGU_____GAG
.........(((((((...............................(((((......)))))......((((....))))....)))).)))..................... ( -8.79 =  -9.04 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:13 2006